'\" t
.TH samtools-dict 1 "2 September 2022" "samtools-1.16.1" "Bioinformatics tools"
.SH NAME
samtools dict \- create a sequence dictionary file from a fasta file
.\"
.\" Copyright (C) 2008-2011, 2013-2018 Genome Research Ltd.
.\" Portions copyright (C) 2010, 2011 Broad Institute.
.\"
.\" Author: Heng Li <lh3@sanger.ac.uk>
.\" Author: Joshua C. Randall <jcrandall@alum.mit.edu>
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.SH SYNOPSIS
.PP
samtools dict
.IR ref.fasta | ref.fasta.gz

.SH DESCRIPTION
.PP
Create a sequence dictionary file from a fasta file.

.SH OPTIONS
.TP 11
.BI -a,\ --assembly \ STR
Specify the assembly for the AS tag.
.TP
.B -A, --alias, --alternative-name
Add an AN tag with the same value as the SN tag, except that a \(lqchr\(rq
prefix is removed if SN has one or added if it does not.
For mitochondria (i.e., when SN is \(lqM\(rq or \(lqMT\(rq, with or without a
\(lqchr\(rq prefix), also adds the remaining combinations of \(lqchr/M/MT\(rq
to the AN tag.
.TP
.B -H,\ --no-header
Do not print the @HD header line.
.TP
.BI "-l, --alt " FILE
Add an AH tag to each sequence listed in the specified
.IR bwa (1)-style
.B .alt
file.
These files use SAM records to represent alternate locus sequences
(as named in the
.B QNAME
field) and their mappings to the primary assembly.
.TP
.BI -o,\ --output \ FILE
Output to
.I FILE
[stdout].
.TP
.BI -s,\ --species \ STR
Specify the species for the SP tag.
.TP
.BI -u,\ --uri \ STR
Specify the URI for the UR tag. Defaults to
the absolute path of
.I ref.fasta
unless reading from stdin.

.SH AUTHOR
.PP
Written by Shane McCarthy from the Sanger Institute.

.SH SEE ALSO
.IR samtools (1),
.IR bcftools (1),
.IR bwa (1),
.IR sam (5),
.IR tabix (1)
.PP
Samtools website: <http://www.htslib.org/>
.br
File format specification of SAM/BAM,CRAM,VCF/BCF: <http://samtools.github.io/hts-specs>
.br
Samtools latest source: <https://github.com/samtools/samtools>
.br
HTSlib latest source: <https://github.com/samtools/htslib>
.br
Bcftools website: <http://samtools.github.io/bcftools>
